General Greengenes Database and Tools Citation:

DeSantis, T. Z., P. Hugenholtz, N. Larsen, M. Rojas, E. L. Brodie, K. Keller, T. Huber, D. Dalevi, P. Hu, and G. L. Andersen. 2006. Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB. Appl Environ Microbiol 72:5069-72.

NAST Alignment Tool Citation:

DeSantis, T. Z., P. Hugenholtz, K. Keller, E. L. Brodie, N. Larsen, Y. M. Piceno, R. Phan, and G. L. Andersen. 2006. NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Res 34:W394-9.

Tree Management Citation:

Dalevi D, T. Z. DeSantis, J. Fredslund, G. L. Andersen, V. M. Markowitz, P. Hugenholtz P. 2007. Automated group assignment in large phylogenetic trees using GRUNT: GRouping, Ungrouping, Naming Tool. BMC Bioinformatics. Oct 18;8(1):402

Original Publication

DeSantis, T. Z., I. Dubosarskiy, S. R. Murray, and G. L. Andersen. 2003. Comprehensive aligned sequence construction for automated design of effective probes (CASCADE-P) using 16S rDNA. Bioinformatics 19:1461-8.

Those citing Greengenes:

• Schloss, P. D., and J. Handelsman. 2006. Toward a census of bacteria in soil. PLoS Comput Biol 2:e92.
• Ley, R. E., D. A. Peterson, and J. I. Gordon. 2006. An extended view of ourselves: ecological and evolutionary forces that shape microbial diversity and genome content in the human intestine. Cell 124:837-848.
• Lecuit, M., E. Abachin, A. Martin, C. Poyart, P. Pochart, F. Suarez, D. Bengoufa, J. Feuillard, A. Lavergne, J. I. Gordon, P. Berche, L. Guillevin, and O. Lortholary. 2004. Immunoproliferative small intestinal disease associated with Campylobacter jejuni. N Engl J Med 350:239-48.